SAO PAULO--OSX Brasil SA, the ship building company of troubled tycoon Eike Batista, filed for bankruptcy protection, the second such filing for a commodities empire that crumbled this year as losses piled up and investor confidence plummeted.

"Parts of Mr. Batista´s empire were a house of cards, and now they are falling," said Guilherme Figueiredo, a fund manager at M.Safra & Co. in Sao Paulo who helps oversee $1.97...